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        <title>Multithreaded gap filling - Peak finder</title>
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        <h1>Peak finder</h1>

        <h2>Description</h2>
         <p>
            This algorithm is a parallelized version of the Peak finder algorithm. If RT correction is needed, perform it prior to this algorithm or use the normal Peak finder.  
		</p>
		
        <p>
            Following alignment, the resulting peak list may contain missing
            peaks as a product of a deficient peak detection or a mistake in the alignment of
            different peak lists.
		</p>
		
		<p>
            The fact that one peak is missing after the alignment does not imply that the
            peak does not exits. In most cases it is present but was undetected by the
            previous algorithms.
        </p>

        <p>
            This algorithm fills the gaps in the peak list when it is possible according with the parameters
            defined by the user.
            The most crucial parameters are "m/z tolerance" and "RT tolerance" which define the window where
            the algorithm should find the new peak. It is centered in the m/z average and retention time average of
            the source peak list. Once the best candidate is found inside the window, its intensity and its shape in RT direction is also
            checked.
		</p>
		
		<p>
            It can also add a previous correction of the retention time in the case it is needed. It will
            change the position of the defined window depending on the prediction of a RT model created
            using all the already aligned peaks in each pair.
        </p>

        <h4>Method parameters</h4>

        <dl>
            <dt>Name suffix</dt>
            <dd>Suffix to be added to the peak list name.</dd>

            <dt>Intensity tolerance</dt>
            <dd>This value sets the maximum allowed deviation from expected shape of a peak
                in chromatographic direction.</dd>

            <dt>M/Z tolerance</dt>
            <dd>This value sets the range, in terms of m/z, to search for possible peak in the raw
                data. Maximum allowed m/z difference.</dd>

            <dt>Retention time tolerance type</dt>
            <dd>Its value can be relative or absolute. The next parameters should be fill depending
                on the value chosen in this parameter. </dd>

            <dt>Absolute RT tolerance</dt>
            <dd>This value sets the range, in terms of retention time, to search for possible peak in the raw
                data. Maximum allowed absolute RT difference.</dd>

            <dt>Relative RT tolerance</dt>
            <dd>This value sets the range, in terms of retention time, to search for possible peak in the raw
                data. Maximum allowed relative RT difference.</dd>
        </dl>
        
        
        <p>
        New peak list showing the filled peaks with a yellow mark.<br>
        <img src="gapfillingResult.png" name="gap filling result">
        </p>

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